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September 2007

September 28, 2007

What is RSS?

On a slightly off topic note:

It's been about 5 months since I started this blog and according to my analytics tools I am gaining more and more readers by the day. Thanks for those who keep coming back and reading, I hope you are finding this blog useful.

I think much of this repeat traffic is due to the subscription features on my blog. If you haven't noticed before there are a couple of ways to subscribe to my blog so that you receive updates whenever I write something new. So far, the most popular method seems to be subscribe by email. You can do so by simply inputting your email address in the box on the right and clicking subscribe. Of course this means that you have to trust that I won't abuse your email address (for the record, I promise I won't EVER, but other bloggers may). Secondly it means that blog updates will be included in your mail inbox. Personally, I receive a ton of email, especially in the morning and I don't like my inbox clogged with a bunch of messages that aren't directly related to my business.

The other way to subscribe is via that orange button on the right. This is a standard RSS button and you'll find it on most blogs.

I tried to explain RSS and subscription in one of my very first posts but if that didn't sink in, here is "RSS in plain english":

There it is. No reason to give up your email address and you get to read your favorite blogs (whether they are about NMR software, music, sports, art, whatever) on your own time. 

Hope that helps. Happy RSS'ing.

Thanks to David Meerman Scott for introducing me to the "in plain english" series.

September 27, 2007

2DNMR.com

Remaining on the topic of Computer-Assisted Structure Elucidation (CASE), one of our most experienced users, Shaun Tennant, has devoted a website to Structure Elucidator where he shares some of his experiences with the software and provides a guide for users including his own tips and tricks to get started.

A must read for any elucidator users out there or anyone interested in how the software works.

Check out his site at www.2DNMR.com

September 25, 2007

Truths and Myths of ACD/Structure Elucidator

I have returned from SMASH after an enjoyable week in Chamonix. What a truly beautiful place. It was great to be in that atmosphere with many nice people from all over the world. I also must applaud the organizing committee for doing another wonderful job of coordination. I already find myself looking forward to next year's SMASH conference.

The week kicked off with our Annual SMASH seminar. Several excellent talks and I would specifically like to thank our guest speaks Jack Newton from Chenomx, Patrick Wheeler for Pfizer, and George Crull from BMS. Most of the presentations are available on the ACD/Labs website, and the rest will be added shortly.

On that topic, I want to specifically point you to a presentation given by my colleague Brent Lefebvre entitled, "Uncovering the Truths and Dispelling the Myths Behind ACD/Structure Elucidator"

There is a lot of great content in here. The two most important pieces in this presentation in my opinion were:

1) Price/Usage- One thing I think people may not be aware of is that ACD/Structure Elucidator is not just one black box product that only serves one function. In fact, it is made up of a bunch of ACD/Labs software products including ACD/1D and 2D NMR Processor and Manager, HNMR Predictor, CNMR Predictor, 2D NMR Predictor, UV-IR, Chrom, and MS Processor and Manager. In other words, the software can be used for much more that just structure elucidation. In fact it can be used every day to view, process, and database different analytical data types, and predict NMR spectra.

2) The Learning Curve- In my opinion, by far the biggest adjustment a Spectroscopist has to make in order to use Structure Elucidator is to adopt ACD/2D NMR Processor as a processing tool. The data work up and in particular the peak picking process is perhaps the most crucial step for Computer-Assisted Structure Elucidation (CASE). I am certainly not implying that 2D NMR Processor is difficult to use, in fact it is quite the opposite. The issue is that it generally requires a spectroscopist to switch over from their favorite vendor software package. This involves them getting used to a new interface, new shortcuts, and new navigation sometimes after years of use. There is certainly an adjustment period, but the rewards are great. Once a user gets used to 2D NMR Processor, they then have the option to take advantage of databasing and structure elucidation tools.

Check out the rest of the presentation to learn more.

P.S. If you would like to see if Structure Elucidator can handle one of your most difficult  problems, submit your data to the challenge here

September 14, 2007

SMASH 2007-This Weekend

I'm leaving today for Chamonix and SMASH 2007. If any of you are attending, be sure to drop by the ACD/Labs booth and say hello.

Also, if you are attending, you are invited to our annual seminar. Details are here.

As I am unsure about my internet connection, I might not be posting next week. But when I return, I will hopefully have some exciting stuff to talk about as a result of the conference.

September 11, 2007

Wolfgang Robien and Modgraph vs. ACD/Labs

Those of you who have been following this blog through it's first few month will no doubt have seen a few posts about the comparisons between ACD/Labs, Modgraph, CSEARCH, and the NMRShift DB. For those of you who have not followed this story but are intrigued, you have a lot of reading to do, starting here:

http://acdlabs.typepad.com/my_weblog/2007/05/nmrshiftdb_acdl.html

If you go to Modgraph's website for example, you will find the following web page:

http://www.modgraph.co.uk/product_nmr_shiftdb.htm

Here Modgraph presents results that show, most notably to this blogger:

Modgraph NMRPredict: 1.40 ppm overall average deviation

ACD/Labs CNMR Predictor: 1.59 ppm overall average deviation

These values correspond to the average deviation of predicted chemical shifts as compared to the experimental values (over 200,000) in the NMRShiftDB. Let me first state that the quoted average deviation for ACD/Labs CNMR Predictor is INCORRECT in this context. The number is correct in a different context. More on that in a moment.

In the meantime, there is one flaw in these numbers that I continue to object to, yet Modgraph continually chooses to pass over. It involves the following statement from their website:

For this evaluation the combined databases from CSEARCH and SPECINFO holding a total of 345,308 reference spectra were used. Based on this higher number of reference spectra a somewhat higher structural overlap between our databases and the NMRShiftDB-testdata has been detected. In order to compensate for this, we have recalculated our overall average deviation of 1.40 ppm using the lower structural overlap as detected by ACD. The value of 1.40 ppm corresponds to 92,927 known carbon environments and 121,209 unknown carbon environments - without this compensation our overall average deviation would be slightly better, but a comparison with ACD's results would be impossible.

Am I the only one who thinks that the bolded part is rather inappropriate and unscientific?

We have acknowledged the overlap between our database and the NMRShiftDB to be 57%. Modgraph declines to share what their overlap is and admits only that it is higher. So in order to compensate for this they have used our lower structural overlap? So what structures and shifts are they removing from their databases to compensate for this overlap? How do they decide which ones get removed?

Irregardless of how this study was conducted, it should be known that the average deviation reported on their website of 1.59 ppm is incorrect in this context as a data point of comparison with Modgraph's number. I have already addressed that number and written a post about it on this blog earlier.

The average deviation of ACD/Labs CNMR Predictor compared to the entire NMRShiftDB (with an overlap of 57% included) is actually 0.96 ppm.

Of course I will re-iterate here my thoughts that I shared in my original posting about this. These reported average deviations (0.96 ppm for ACD/Labs and 1.40 ppm for Modgraph)  are likely not the best measure of how well NMR prediction software will perform for an end user. Why? Because as clearly stated, these numbers are based on an experimental dataset (the NMRShiftDB) that has a 57% overlap with the databases in the prediction engines.

So unless you, the end-user can expect a very significant overlap between your own compounds and the NMR predictors (57%) you shouldn't expect this kind of accuracy. In reality, chances are you are working with novel chemistry and the majority of your compounds are completely novel and thus not represented in a prediction softwares database.

In my opinion, we have come up a best practice for NMR prediction validation. Not only do we provide an average deviation for the entire NMRShiftDB dataset (0.96 ppm and acknowledging a 57% overlap), but we also provide a a validation study on the completely novel chemical shifts. This study evaluated only the chemical shifts that are not present in our database (the other 43%).

Modgraph has yet to produce a study consistent with the second approach (that is, a study on completely novel chemical shift not represented in their database). In fairness to them, it can be argued that this is not a fair comparison either as we would likely be comparing two completely different data sets with completely different structures. Our overlap is not the same after all.

Nonetheless, ACD/Labs has provided the public with both numbers for their reference. The bottom line, is that Modgraph has chosen to publish some number that doesn't have a clear explanation behind it. It neither represents an evaluation of the entire dataset, nor one without any overlap. Their reported number is somewhere in between and they have declined to offer details. If they  produced an average deviation for  the entire dataset (including all overlap) or the results of a dataset excluding any overlap, it would most definitely be different than 1.40 ppm value they have quoted. All we hear from them is that if they didn't compensate for the difference in overlap between ACD/Labs and Modgraph, their results would be SLIGHTLY better. 

That's fine, and while I question their experimental method of removing chemical shifts to compensate for the difference between ACD/Labs and Modgraph's overlap, this is the study they have chosen to go public with. So in the end the final results are:

Modgraph NMRPredict: 1.40 ppm overall average deviation

ACD/Labs CNMR Predictor: 0.96 ppm overall average deviation

September 05, 2007

The Price of NMR Software

So I will be presenting at our annual seminar at SMASH in a few weeks, and I always enjoy doing so. One thing I have picked up on over the years when presenting in our seminars, in addition to other seminars, is that look of curiosity and waiting that appears on the audience's faces as we go from slide to slide. That look that can be translated to, "How much does this stuff cost?"

I am going to talk a little about a fairly touchy subject. Pricing.

It's no secret that ACD/Labs does not share it's pricing online while some of the other vendors of NMR software do. Sometimes we take criticism for that. I have also heard many times from many people that ACD/Labs software is really expensive.

I am not going to hide those conversations, they are out in the open right here and right now.  But the real question is, "what defines expensive?"

I think it is very subjective. I happen to think that $400 for a purse is very expensive. My wife may disagree. I think that $5000 for a guitar is not expensive. My wife definitely disagrees. It's subjective.

But we are talking about NMR software after all. I think when you think about pricing for software you have to look at many different variables.

So there are  a couple of questions I will try to answer to somewhat address the "elephant in the room":

1) Is our software expensive?

Some people have a pre-conceived idea that no matter how good a piece of software is, it shouldn't cost more than $500. Heck, some will argue that all software should be free. I disagree with this for a number of reasons, but let me start by outlining some of the things that have to be considered when determining the price of software. To name a few:

- The cost of developing the software
- The cost of maintaining the software. If you sell it for less than the cost of development and improvement, than it becomes very difficult to maintain the software, add new products and features, and fix bugs. If the software company goes out of business because they can't maintain and improve their software, everybody loses.
- The cost of supporting the software and the customer base. i.e. product management, development, technical support, sales, marketing, production, etc.
- The market. How big is it? Is there competition? Are they better than you? What can they afford?
- The costs the consumer encounters for deploying the software in their institution (i.e. installations, training, etc.)

This kind of thing is of course not unique to ACD/Labs. It is the similar to what other industries have to consider when selling books, education, or pharmaceutical drugs!

So answer the question Ryan, "is your software too expensive?" Well I would say no. But of course I would, I am an employee of ACD/Labs after all, I can't admit that it is expensive, can I? The truth is that I have spent a lot of time in my last 4 years speaking with customers and users of our software. I have heard excellent stories about how valuable our software is, how much time it has saved, and how much it has benefited their research, students, departments, etc. One of my favorite comments from a Structure Elucidator user was, "If the software can either dereplicate or elucidate even one of my unknowns, it has paid for itself!" In instances like these, I don't think the software is too expensive because the benefits these groups are receiving have far outweighed the cost it took for them to obtain the software.

Unfortunately, there are also cases where users just haven't found the software useful for their research, or haven't even gotten around to installing it yet. In those cases they might have considered the software not valuable and thus the upfront cost was not justified. It happens. We try to prevent it as much as possible, but unfortunately it is unavoidable in some cases. 

I think we have very good software. We work very hard on the development of good software products. We fix bugs and add new things year round and we release a MAJOR version of the software every year with new enhancements and features. With the help of NMR spectroscopists and scientists around the world, we will often identify market needs that allow us to further innovate and augment our core software through new software product offerings. We have been in existence for over 11 years and we continue to make good software and we continue to improve and innovate from version to version. We work hard to make our different modules integrate with each other so users can extend the capabilities of the software. Finally, we sell the software. We have many, many customers from all over the world. To name a few:

http://www.acdlabs.com/clients/
http://www.acdlabs.com/educators/acadclients.html

We've sold to these companies and institutions and we have survived more than 11 years in this industry selling and supporting our software in many of the above institutions and more. I don't think we would have come this far if our software was flat out "too expensive".

Finally, I think I have to acknowledge the market that we are in strictly from an NMR software perspective. There are several companies who primarily develop NMR software out there:  Acorn NUTS, Mestrelab, Modgraph, NMRTec, to just name a few. But I don't think any of these companies cover the scope of the NMR Spectroscopy applications like we do. This is not a criticism of them, they just have a different business and strategic focus for what they want to achieve with their software. We offer NMR processing, prediction, databasing, automated structure verification, computer assisted structure elucidation, high-throughput quantitation and verification, and enterprise solutions. Furthermore, we support a wide range of other analytical techniques so it is possible (with the correct modules in place) to view, process, and database NMR, MS, Chromatographic, UV-IR, (and more) data all in one place. In other words whether you are just starting with our simple NMR Processor, there is the opportunity to expand the solution in many different ways. I don't think this is possible with many other NMR software companies. Of course some people aren't interested in the complete solution. That's completely understandable and as a result you can just purchase what you need. For that I think our individual NMR processing, prediction, databasing (and other) packages are very competitively priced with other similar products in the market. Check out the quotes from some of these press releases, there is a common theme in all of them:

http://www.acdlabs.com/clients/pr_nmr_1206.html

"All of our chemists are now able to manipulate their NMR data at their convenience which has eliminated the lengthy line-ups we used to face in our walk-up lab. ACD/Labs was able to provide us with great tools that meet our needs and were competitively priced."

http://www.acdlabs.com/clients/pr_bristol0806.html

"ACD/Labs were also able to offer us a competitively priced and flexible site license that meets the range of access requirements of both the students and staff members at Bristol."

http://www.acdlabs.com/clients/pr_kalexsyn0506.html

"All of our chemists are now able to manipulate their NMR data at their convenience which has eliminated the lengthy line-ups we used to face in our walk-up lab. ACD/Labs was able to provide us with great tools that meet our needs and were competitively priced."

It of course becomes a bit more difficult to price some of the bigger products because there is simply nothing comparable to it in the market. And generally these bigger products are subject to huge amounts of development time (i.e. ACD/Structure Elucidator and ACD/2D NMR Expert).

Is ACD/Labs software expensive?

No. Some of it is, yes...but I think it is expensive for a reason. And that of course is subjective, if you receive the benefits that we claim from the software, then it is definitely not expensive, in my opinion.

The point I am trying to get at is that the value of the software is what you yourself get out of it. If you have a major problem with a crowded instrument room because all you have is one seat of the vendor's processing software available, then deploying offline processing for all of your chemists would probably have a significant amount of value to it.  Then again, if you don't have this problem but you view it as a luxury to have desktop processing for everyone, then perhaps you would think it is too expensive.

2) How much is our software?

Our company has a policy regarding not publishing our prices and it is not in my right to publish those here. That policy has been implemented for many reasons, and it does raise an interesting question.

Why wouldn't we share our prices publicly?

Well I think that the logical response most people would come to is, "because they are too expensive"

I don't believe that's the case.

In fact, years ago, we DID publish our pricing on the website, we even had a webstore for all of our products. Unfortunately, this  was not successful. In fact, we continued to sell software the way we do now, through people contacting our account managers and having a discussion about their wants, needs, and desires.

And this, leads to one of the problems we encountered by posting our pricing online. It's one of the drawbacks of having 100+ different products. Potential customers tend to get overwhelmed by the number of choices and they want to make sure that they don't pull the trigger on a product that they don't need. So they simply write an email or pick up the phone. Furthermore, the pricing of our products is not always static. There are often special discounts on certain products, and bundles depending on whether you are a new customer, current customer, an academic, the number of products or licenses you want to buy (do you want a copy for everyone, or would you like 15 people to share 5 copies), etc.

Therefore, as a company, we have resigned ourselves to the fact that we need to involve the sales person in all sales discussions. In doing so we can ensure that they can take the prospective customer through different options and ensure they get set up with the best solution for their needs at the best possible prices. I think that's a good thing. We pride ourselves on good customer interactions and customer service, and I hope that some of you have benefited from that already.

If you have made it to the end of this entry, I am grateful for your attention. I hope that I have at least somewhat addressed the elephant in the room, lab, or blogosphere.