Tip of the day #4: Increasing the intensity of 2D traces
February 5th, 2010
You can easily increase or decrease the intensity of the traces just by hovering the mouse over the trace and scrolling the mouse wheel.
Tip of the day #3: Full View
February 3rd, 2010
This feature will bring up a miniature view of the entire working document with the active area of the spectrum highlighted in blue.
You will be able to toggle the Full View window by using the F2 key. This will allow you to get a ‘Super Fast’ panning.
If ‘Apodization’ is selected, then the ‘Full View’ switches to show the FID and the effective window function. This allows you to manipulate the FID and observe the effect on both the FID and the spectrum.
How MestReC was born
January 27th, 2010
Over the years, many of our users have asked about the history of MestReC and the early days. Now that we are celebrating the 5th anniversary of our company, Santi has already written in the Mestrelab blog about the birth of Mestrelab as a company, but this omits the early years of MestReC, which I will cover in the oncoming posts.
When I started the MestReC project, back in 1995, I was not really aware of all the consequences it would eventually have. At that time, I had just returned from England and had no clear ideas on what to do with my professional career. In principle, the most attractive option for me was to carry on doing organic chemistry research and to pursue a PhD as I had had a very good experience in that field in the group of Prof. Paul Jenkins in Leicester. However, my thoughts were so scattered that I even considered the possibility of earning a living playing drums in a rock band :-). Fortunately for the hearing health of many people, I soon abandoned that crazy idea and decided to keep my focus on the scientific arena.
And it was at the moment, whilst I was enjoying a period of pleasant procrastination, that Javier came to me to propose a devilish project for off-line NMR data processing and analysis which he named MestReC (more about the name in a moment). I knew almost nothing about signal processing (other than basic Fourier Transform theory) and my experience as a programmer went back to small applications that I developed in Pascal whilst at Secondary School. But ignorance is bold and, in this case, it turned out to be our best friend, because I was brave enough to accept the project. Needless to say that Javier was also quite reckless to trust someone like me to carry out such a project 
Just before I continue with the story, a quick note on the name MestReC. This is an acronym for Magnetic Resonance Companion, as Javier was very insistent that the software should be very easy to use, a tool that would work on the data ‘with’ its users, helping them and accompanying them on the research journey. At the same time, ‘mestre’ means teacher in our local language, Galician, so the name also refers to the potential educational qualities of the software and to its geographical origin. As if fate had an input in it, of course, the C could also refer to the fact that the software was written in C/C++, but that was not the case initially and this consideration did not come into it.
Right after Javier introduced the project, and as an evident sign of silliness, I said, ‘yeah, no problem, this is something I can do in less than 6 months’. At the present time, after more than 14 years of development, I have come to the realization that it is a never ending project. Anyway, we still remember that memorable day back in late November 1995 when we saw for the first time an FID displayed on a DOS window after a few weeks trying to decode the cryptic data generated by our 250 MHz spectrometer equipped with an Aspect 2000 console. Funnily enough, we selected one of the most difficult formats to start off the project. The integer numbers were 24 bits long (3 bytes) with different byte ordering and the floating point numbers did not follow the IEEE 754 standard. But after some hacking around with some algorithms written in Assambly Language embedded into a Pascal application, we managed to create our first NMR data converter.
After that little but encouraging success we thought that the next step, Fourier Transform of the FID, should be something much simpler. Once more, our initial decision of using data from the Aspect 2000 turned out to be quite unfortunate in the short term as I will explain in a moment, but from my current perspective, I have to admit that it was a very beneficial circumstance as it forced us to ponder on our knowledge of the various protocols for NMR data acquisition and to delve deeper into Fourier Transform theory.
Without going into too much technical detail, the problem with the data set we were working with was that it required a real Fourier Transform (as opposed to a complex Fourier Transform) as the data was acquired in the so-called sequential mode (which means that the real and imaginary components of a complex value were not sampled simultaneously but rather one after the other using one single ADC). When we learnt all the tricks to transform a sequential FID, we produced our very first version of MestReC (version 0.1). It was of course a very primitive one, developed in Pascal (with those Assambly routines for data file parsing) which worked in DOS mode and , in addition to FT, it included basic weighing functions (Exponential and Gaussian) and manual phase correction. Obviously, it was intended for 1D NMR data only. Unfortunately, as the opposite would be great if only for nostalgic reasons, no part of this DOS/Pascal application has survived.
Of course, we knew that we would get nowhere with an application for DOS. It was precisely that year when Windows 95 rolled out and this appeared as a unique opportunity for us. Leaving all graphical enhancements aside, the greatest benefit we saw with Windows 95 was the 32 bit arquitecture which made programming of memory intensive software (such as NMR apps) much easier than 16-bit based Operating Systems (MS-DOS, Windows 3.x, etc). Well, I reckon that Windows 95 was not a 100% 32 bit OS, but for our purposes that did not really matter.
So we focused our development efforts on Win95. Another decision we had to take at that point was whether we should keep programming in Pascal, the language I felt more comfortable with, or rather switch to something else. I now remember that I spent a few hours in a library close to the Chemistry faculty taking a look at different programming books and I found a rather voluminous book by Charles Petzold titled “Programming Windows”. I decided to buy it and spend the Christmas holidays going through it. It was a great read and convinced me to learn and use C as the language for the new Windows 95 version of MestReC. This meant that I had to port the old Pascal code to C which basically consisted in starting the project nearly from scratch.
In a couple of months we managed to get a first prototype of the application working (BTW, this was possible thanks to the great support I got from Giuseppe Balacco, developer of SwanMR). In addition to supporting Bruker Aspect format, this new Windows version imported Bruker X32, Varian and Nuts file formats. As for its processing capabilities, it included basic tools such as different weighing functions (Exponential, Gaussian, Sine Bell), Fourier Transform of both sequential and simultaneous FIDs (real and complex FT), phase and baseline correction and some basic analysis tools (peak picking and integration).
Maybe the first ever NMR spectrum processed in MestReC 1.0
To the best of my knowledge, this was the first Windows 32 bits (Win32) native application for NMR data processing. Despite being a very simple application, it soon turned out to be a very useful piece of software for many people, not just in our department, but also in several universities around the world.
More on what happened after this first release in my next post.
5 years of Mestrelab - The future
January 27th, 2010
So, over the last few weeks both me and Carlos have blogged extensively about the past and about how Mestrelab came to be and to grow into what it is today. But of course, although 5 years looks like a long time when you think about it, it really is not, and specially for a company, and therefore we are now staring at the next 5, and hopefully 10, 20, 50 years (not me personally for the latter, mind). We have many options, and many ideas, possible business models, potential projects, and it is of course hard to make decisions and to give up some of these to make the others possible. And we should not only do what we think is best, but we should listen to our loyal customers and find out what it is that they would like us to do, and the business offers they would support from our company.
We have a great, young and enthusiastic team of people with a wide range of skills in the scientific software field, and with the capability to learn fast and to take new projects on. We also now have a very exciting network of likeminded collaborators who allow us to stretch our development efforts far beyond our internal capabilities. And we have the desire to continue to expand our offer and to continue to fulfil our customers’ needs. These are all great assets to fuel future growth.
However, there are some things we really not want to do. We don’t want to compromise with the quality of our product because of overstretching it, we don’t want to reduce the quality of our customer service because of cost reductions or delocalizations (don’t you love these words!). And we don’t want to stop having fun while we work on a field we find, to many people’s surprise, very exciting!
There are some things we know we want to do, or which we are already starting to do:
- We want to continue to improve the capabilities of our software to handle and analyze different experiments and to support different applications, and we are always open to hearing about new or different things our users would like to do with the software. Write to us with new applications and feature requests in our current fields and we will consider them.
- We want to continue to build the LC/GC/MS plugin as a complimentary plugin to the NMR one, but also as a high quality software application in its own right, focused on user workflow.
- We want to push the potential of our processing and analysis capabilities in the area of automatic structure determination (Verification). We are making very good progress in this area with the help of the ineffable Stan Sykora, and we are very excited about the announcements we are likely (or hopeful) to be making in the near future. Watch this space, and let us know if you would like us to keep you posted on progress here!
- We want to combine the information obtained by NMR and LC/MS or GC/MS on this automatic structure determination effort, to gain as much reliability as possible.
- In order to continue to follow the Mnova ‘integrated software suite for handling of analytical data’ concept, we think that including databasing capabilities in Mnova will add great value to our users, and are therefore creating a database environment to handle analytical data using Mnova as the client to drive saving, indexing and searching. We are very keen to hear from users who would be interested in such databasing capabilities, and to know about the main needs/features/applications people have in mind for such a tool. Please write to us if you would like to know (or would like us to know) more.
- There are many things we could do, and it would be great to hear about what you, our users, think we should be focusing on. We see many possibilities in molecular structure handling and storing, in automatic management of analytical data, in plugins for the computation of additional physical properties, in processing and analysis of data coming from additional techniques, etc. The flexibility of the Mnova interface should allow us to integrate many of these capabilities without compromising the integrity of Mnova as a single software package, and this is exciting and something we would like to exploit for the benefit of the Chemistry and Biology communities. We also want to know if you think there are any third party softwares we should be integrating closely with (LIMS and pipeline management systems, etc.). Finally, we are very keen to hear about how you feel we may improve our customer service, become more accessible to our users and which conferences and events we should make sure we support in our annual calendar.
So, this is your chance to make sure our company continues to go the way you would like it to for the next 5 years. We very much look forward to hearing from you! (Use the comments of this post, our email support[at]mestrec.com or the contact form at our web page.)
Tip of the day #2: How to measure coupling constants
January 25th, 2010
It is very easy to measure coupling constants with Mnova, just by using the Crosshair feature, which can be accessed by pressing the <C> key.
The crosshair includes information about the chemical shift and the intensity of the peak and also allows you to measure distance between peaks (or coupling constants) by clicking on the left mouse button and dragging to the desired peak.
Tip of the day #1: Zoom in modes
January 21st, 2010
Flexibility when visualizing data is very important in any graphical analytical program. One of the main capabilities from this point of view is zooming, and a number of ways of zooming are available in Mnova. There are in fact three ways to ‘Zoom In:
- Vertical
- Horizontal
- Box
You can toggle from one zooming mode to another just by pressing the <Z> key. The video below illustrates these different zooming modes.
In addition, a zoom lens of 20% will be obtained by clicking on the left mouse button (after having selected the ‘zoom in’ feature by pressing the ‘Z’ key or selecting it from the toolbar or ‘View’ menu).
How to get the most out of Mnova: Introducing the ‘Tip of the Day section’
January 20th, 2010
After speaking to many of our customers at conferences, training sessions, etc., we noticed that a great proportion of our users were not very familiar with some of Mnova’s most interesting features.
Of course, you can always visit our Resources Section on our web page or contact our support team when you want to find out more about a specific issue.
However, the purpose of this section is to create a series of short articles (tips) that will help you discover essential Mnova functionalities such as: How to analyze 1H-NMR spectra and create multiplet reports ready for publishing in journal specific format, different methods for zooming, how to efficiently use the full view feature in the program, how to change the intensity of the traces of 2D NMR, and many more.
We have already published the first one: Zoom in modes, so follow this link to have a look at it.
5 years of Mestrelab (year 5) - The present
December 14th, 2009
I finished the last post writing about our move to the new office, and about how this allowed us to grow the team further, which we immediately started doing, with the additions of Dani, our internet marketing specialist, and Jose, Michael and Esther to the development team, taking our headcount to 15 people during 2009, and extending our areas of expertise further beyond NMR.
The early part of the year was marked by the 50th ENC, held at Asilomar. We arrived at ENC after also having a booth at the ACS Spring in Salt Lake City, and once at ENC we graduated into a full blown suite, Curlew, which has an excellent location in the middle of the Asilomar grounds, and which was very popular with visitors throughout the conference. We look forward to returning there many times in the future. The ENC conference was great, with many very interesting sessions, including an excellent, and very nostalgic, historical session with many of the big names in NMR as presenters. It was a privilege to be able to attend it.
After ENC, Chen and I went back to China and started a very positive collaboration, with our Chinese distributor, TLWB, a company with a large presence in the Chinese NMR community who has been doing a great job at promoting our software and opening new business opportunities. I blogged extensively on my trip to China on this blog at the time, so I will not add anymore here.
Also on the blog you will find summaries and stories about many of the conferences were we exhibited this year, ASMS in Philadelphia, ACS in Washington, CoSMoS in Boston, EUROMAR in Goteborg, IMSC in Bremen, ESOR in Haifa and SMASH in Chamonix. They are all also covered on the blog if you would like to find out more about our activities there.
The main event of the year, from a product point of view, was the launch of our LC/GC/MS plugin for Mnova, in September. This makes Mnova not only multivendor and multiplatform, but also multitechnique, representing a first step in our original objective when designing the application, thought out not only as an NMR software, but rather as a ‘Chemistry Software Suite’. Mnova MS has been developed in collaboration with Sierra and has met with an excellent reception from our customer base, with many people keen to evaluate it and many purchasing licenses already.
Towards the end of the year, we also passed the milestone of 50 academic campus licenses, many of them held by some of the most prestigious Universities in the World, and a number of corporate companies have during this year chosen Mnova NMR as their NMR processing tool of choice, continuing with a trend which we saw started last year. So, our project is meeting with great commercial success, the software is ever more popular, and this is giving us the opportunity to keep building both our internal development team and our network of collaborations, which will result on a series of exciting product launches and new features in the near / mid term future.
The last 5 years have been a very exciting ride, which has been made possible by the confidence and support of our many users (in excess of 20,000 paying licensees around the World), by our collaborators and by the hard working and dedicated team at Mestrelab. To all those, the Mestrelab founders want to extend a very heartfelt thank you. We look forward to continuing to work towards delivering excellent quality Chemistry software for the community, and to continuing to work in an inspiring market filled with creative and challenging (in a positive way) customers.
Over the next few days, I will publish one more blog, on the future, but this will be more filled with questions than answers (although there may be a few of those). We have some ideas about where we are going, but we really want to ask the community, once more, where they think we should be going and which needs we should be aiming to cover.
I hope you have enjoyed this historical series on Mestrelab, I cannot believe 5 years have gone by already! Any comments or questions are welcome.
We are celebrating Mestrelab’s 5th anniversary!
We are celebrating our first 5 years in business. This post belongs to a series of posts where Santi is summarizing what we did and this 5 years and what we plan to do in the future.
5 years of Mestrelab (year 4) - US, China and Mestrelab’s international expansion
December 11th, 2009
I start the post on 2008 mentioning something I forgot in 2007, which was the acquisition by Mestrelab of a new premises. We could see that Carlos’s apartment would soon be outgrown, and we therefore invested in a new office close to the centre of Santiago de Compostela. What we bought was a shell and therefore, part of 2007 and the whole of 2008 would be spent waiting for builders to finish the work they had undertaken to fit it for our purposes. Many say Spanish builders have suffered due to the financial crisis which would unfold later in the year, and that is undoubtedly true, but from our perspective, if we gave this kind of response to our customers, we would not expect to remain in business. 2008 was therefore frustrating from that point of view, as our in-house growth was somewhat curtailed by the lack of office space to place new developers, and therefore our headcount remained stuck at 10 whilst we fought with the builders.
However, we grew in other ways. We grew in product range, as our agreement with Sierra Analytics Inc, also finalized in 2007, to develop an LC/GC/MS plugin for Mnova started to give us a more general appeal for chemists outside the specific NMR community, and thus made us start going to more general conferences. 2008 therefore saw our first attendance at an ACS National Meeting, at New Orleans in April, soon after having our first suite, the Forest Lodge, at an ENC, which was back at Asilomar for its 49th edition. So, we were growing in our attendance to conferences, and also in the size of our presence there. And we were also growing geographically, with our opening of an office in the US, in San Diego, CA, after reaching an agreement with Dr. Chen Peng, who became our new Business Development Director for US and China. We also attended, as vendors, our first MS specialist conferences, with ASMS in Denver and CoSMoS in San Jose being the first ones, whilst repeating at the ACS with a stand at the Fall Meeting in Philadelphia. As for NMR conferences, in addition to ENC, we also attended EUROMAR in St. Petersburg (great city, at least as a leisure visitor), SMASH in Santa Fe and the Spanish Bi-Annual NMR Meeting, held in Seville.
So, whilst World economies where rapidly swinging from a fear of inflation, with the petroleum barrel edging towards $150, to a recessionist panic after the collapse of Lehman Brothers in September, Mestrelab kept growing and expanding its range. In a year when the Lightning Bolt flew in Beijing and when the Baltimore Shark astounded us all by surpassing Mark Spitz, we were also racing, in our own fashion, towards a more international presence, which even took us to China too, which Chen and I visited in a business development trip at the beginning of November. Thus, as well as starting to open some significant business with the Chinese CRO and pharmaceutical industry, I was in Shanghai to witness the results of the US General Election, which saw Barack Obama become the 44th President and maybe justify his ludicrously awarded Nobel Peace Prize by the single fact of replacing George Bush (not that Bush could have stayed, showing one of the great features of the American Constitution). With this event, our conversations with American scientists became a lot more fluent, as they no longer felt the need to start by apologizing and explaining that they had nothing to do with the election of their incumbent president ;-).
New Office
Our New Office entrance door
And finally, in December 2008, in the middle of World financial turmoil, and just after the inauguration of President Obama and of the Large Hadron Collider, at CERN, we also inaugurated our new office, to which we moved on 12th December, thus gaining some much needed breathing space (anyone who visited us during 2008 will vouch for that) and the ability to grow our team again, which we started duly doing at the beginning of 2009, but that is another story or, at least, another post!
We are celebrating Mestrelab’s 5th anniversary!
We are celebrating our first 5 years in business. This post belongs to a series of posts where Santi is summarizing what we did and this 5 years and what we plan to do in the future.
5 years of Mestrelab (year 3) - The advent of Mnova
December 9th, 2009
2007 was not only the year of the accession of Bulgaria and Romania to the EU, and of Slovenia to the Euro, but it was undoubtedly a year of changes in leadership (Just take a look at this list, which is only the main, or best known, leadership changes in that year: Ban Ki-moon took over Kofi Annan as UN Secretary General, Nancy Pelosi became the 1st Female Speaker of the US House of Representatives and, more importantly, the first democrat speaker for a while, Nicolas Sarkozy took over Jacques Chirac as President in France and Gordon Brown over Tony Blair as UK Prime Minister, Yasuo Fokuda took over as Prime Minister of Japan from the resigning Shinzo Abe and President Vladimir Putin did the same in Russia over resigning Prime Minister Mikhail Fradkhov, paving the way for Dmitry Medvedev to become the new President, John Howard was finally defeated in an Australia Election by Kevin Rudd and Cristina Fernandez de Kirchner became the new President of Argentina). And Mestrelab set off at the beginning of the year with the intention of continuing to work towards a change of commercial leadership in the NMR, and eventually Analytical Chemistry, software market. And to do so, we continued to work on our already not so secret weapon, Mnova, which we were convinced would at least establish a clear technical leadership in the industry.
But even before that, during February, and just after Estonia had become the first country to stage a General Election over the internet, showing the shape (and more importantly, the place) of things to come, we acquired an interest in the internet World ourselves, with our acquisition of a stake in eMolecules, the Southern California based search engine and ecommerce chemistry tool which is set to become the Amazon of chemistry. This was very exciting for us, as we were and remain convinced that eMolecules will bring great value to the same customers we are servicing with our software.
So, with a stake of eMolecules under our belt, Carlos, Nik and I set off for Daytona Beach, and the 48th ENC, ready to finally launch, and unveil, Mnova. The first commercial version of Mnova, 5.0.3, was enthusiastically received by most ENC attendees who visited our booth, and this greatly encouraged us and reaffirmed us in our conviction that we were following the right path with its development. NMR spectroscopists loved the flexibility afforded by its multipage interface, its multiplatform nature, the possibilities open by its architecture and by its unmatched scripting capabilities. During this ENC, we also signed a distribution agreement with Varian for Mnova, which we saw as further recognition by one of the main players in our market of the fact that Mnova was starting to be regarded as the best software tool available. Daytona was therefore very encouraging on that front, although of course, the sight of thousands of 4×4 trucks sporting massive fridges and sound systems being driven into the beach everyday by people who obviously don’t like to walk or be in contact with the sand, even on the beach, was fairly discouraging for Europeans long engaged in the climate change debate. Of course, the discovery, simultaneously to the ENC, of Gliese 581c, an Earth-like planet potentially capable of sustaining life in constellation Libra was a great relief for us.
After ENC, we attended an excellent EUROMAR and Iberoamerican meeting at Tarragona, Spain, where we also had an exhibitor booth, and then the first SMASH meeting held at Chamonix, in France, an spectacular setting used again in 2009 (and it seems as if planned for 2011) and on which I have blogged elsewhere. Chamonix saw the consolidation of our tradition of holding User Meetings at SMASH, with a meeting attended by over 60 people, who outsized the room we had booked for its celebration. Mnova kept proving extremely popular, and our software sales took a huge hike, still well below those of Harry Potter’s last instalment, ‘The Deadly Hallows’, which sold 11 million copies during its first 24 hours in the market and left us thinking ‘if only’ ;-). But we were also doing fine, and industry were starting to take us really seriously, with the end of 2007 seeing Worldwide adoption of the software for general deployment by a couple of very prestigious, multinational pharmas and biotechs which I don’t have permission to mention. All this meant we could keep growing the team with confidence, and we did so with the addition of Pablo, a new Applications Chemist, and Santi, a beautifully named software developer. NMR For All also kept going strong, although of course, it paled into insignificance when compared to Sheikh Mohammed bin Rashid al-Marktoum’s largest ever charitable donation of €7.41 bn (this was of course when things in Dubai were going better).
So, with Mnova well established, eMolecules on the road and our first corporate deals under our belts, and whilst witnessing the assassination of Benazir Bhutto in Pakistan, the abolition of the Nepalese monarchy, the signing of the treaty of Lisbon and the accession of 9 former Easter countries (well, 8 plus Malta) to the Schengen Treaty, and with a careful eye on the UN Climate Change Conference held in early December (déjà vu) in Bali, we waved goodbye to 2007 and marched, full of enthusiasm and hope and with an strengthened Mestrelab, into 2008. And that will be my next post.
We are celebrating Mestrelab’s 5th anniversary!
We are celebrating our first 5 years in business. This post belongs to a series of posts where Santi is summarizing what we did and this 5 years and what we plan to do in the future.
