To be honest, I have not described all the details. I feel I have been pedant enough. There is another trick yet. If you select multiple items, the preview window shows additional controls. Without explaining everything, here is the picture:
Tuesday, 25 November 2008
Wrap Up
When you split an article in pieces on a blog, they appear in reversed order, so it's not a great idea. A summary helps:
To be honest, I have not described all the details. I feel I have been pedant enough. There is another trick yet. If you select multiple items, the preview window shows additional controls. Without explaining everything, here is the picture:
To be honest, I have not described all the details. I feel I have been pedant enough. There is another trick yet. If you select multiple items, the preview window shows additional controls. Without explaining everything, here is the picture:
Tuesday, 18 November 2008
Coda
In this fourth and final part of the article, we'll discover the flexibility of the metadata system. For example, let's say you don't like the slideshow. A single picture is enough. You want, however, to inspect the metada. In the second part we learned that the command "Get Info" satisfies this need. The new command "Quick Look" can generate a different representation. It shows the same information (more or less), with an HTML layout and much larger fonts. In other words, it's more readable:
There is also the opposite way of doing things. Let's say that you want to see your list of files in text form, without icons and thumbnails, without the coverflow effect, but you want to see the preview of your files nonetheless. Here again the "Quick Look" command comes to the rescue. It opens a glassy, dark-grey window, that acts as an ispector. When you select a file, the preview window shows the internal pages. You can use the scrollbar (or the keys PageUp and PageDown) to move through the pages. If you select a different file, its contents are automatically shown.
The preview also includes an optional Full-Screen mode, when all the other windows are hidden and the background is black. You activate this mode by clicking the symbol with two white arrows. The full screen-mode is too large to be shown here.
None of things described in my article will help you to make a discovery. That's normal. Do you ask to the computer hardware to increase the number of your publications? I think not. Why, then, should we ask such a thing to the software?
There is also the opposite way of doing things. Let's say that you want to see your list of files in text form, without icons and thumbnails, without the coverflow effect, but you want to see the preview of your files nonetheless. Here again the "Quick Look" command comes to the rescue. It opens a glassy, dark-grey window, that acts as an ispector. When you select a file, the preview window shows the internal pages. You can use the scrollbar (or the keys PageUp and PageDown) to move through the pages. If you select a different file, its contents are automatically shown.
The preview also includes an optional Full-Screen mode, when all the other windows are hidden and the background is black. You activate this mode by clicking the symbol with two white arrows. The full screen-mode is too large to be shown here.
None of things described in my article will help you to make a discovery. That's normal. Do you ask to the computer hardware to increase the number of your publications? I think not. Why, then, should we ask such a thing to the software?
Slideshow
In the second part of this article we saw the coverflow effect. In this third part we'll see what happens when we move the mouse near to one of the thumbnails.
Two arrow controls appear. They let us browse the internal pages of a document. In the case of a spectrum, the pages can correspond to some important details or to user comments. Alternatively the user may choose to change the display mode. In our example, the integrals are shown on the first page only, the peak frequencies on the second page only.
In practice, the computer has automatically generated a slideshow presentation for you. This becomes very useful indeed when you want to browse your spectra of yesteryear, or when your boss asks you how are things going and you obviously have no time to prepare a PowerPoint presentation.
If you click the above pictures you can see them at their natural size.
Two arrow controls appear. They let us browse the internal pages of a document. In the case of a spectrum, the pages can correspond to some important details or to user comments. Alternatively the user may choose to change the display mode. In our example, the integrals are shown on the first page only, the peak frequencies on the second page only.
In practice, the computer has automatically generated a slideshow presentation for you. This becomes very useful indeed when you want to browse your spectra of yesteryear, or when your boss asks you how are things going and you obviously have no time to prepare a PowerPoint presentation.
If you click the above pictures you can see them at their natural size.
Metadata
It's not easy to obtain the permission to show a nice spectrum. For this article I have downloaded a collection of spectra of a standard compound from the Biological Magnetic Resonance Data Bank. They are not very nice but can serve my purpose. I have also processed the spectra to highlight the relevant information.
Now I'll show you what is visible after you close the processing application. All the snapshot are taken while working with the operative system. I have uploaded very large pictures, so you don't lose too much (you'll only lose the animation effects). The blog shows them at a reduced size, but if you click a picture, the full-size original appears.
As a starting point, I have selected a file, without opening it; the command "Get Info" shows this panel:
This is only moderately useful, because selecting a file is already a time-consuming operation (you have to navigate through the folder hierarchy). The good news is that the computer can find the spectra for you, if you specify the same properties. This is the job of the command "Find". For example, we can ask the list of all the files relating to substances of general formula C5H7NO3:
Yes, the computer understand a chemical formula! Such a search is not restricted to NMR documents. We can however add more conditions to restrict the search, how many conditions we like. For example:
Every time I type a single character the list of results is updated (live). There is also the option of displaying an animated list. It's a cinematic effect that's very characteristic. If you have ever seen iTunes or the iPhone you know what I mean. On my blog I am limiting myself to displaying static pictures, however. Here is how my spectra look like:
And this is only the appetizer! [continues...]
Now I'll show you what is visible after you close the processing application. All the snapshot are taken while working with the operative system. I have uploaded very large pictures, so you don't lose too much (you'll only lose the animation effects). The blog shows them at a reduced size, but if you click a picture, the full-size original appears.
As a starting point, I have selected a file, without opening it; the command "Get Info" shows this panel:
This is only moderately useful, because selecting a file is already a time-consuming operation (you have to navigate through the folder hierarchy). The good news is that the computer can find the spectra for you, if you specify the same properties. This is the job of the command "Find". For example, we can ask the list of all the files relating to substances of general formula C5H7NO3:
Yes, the computer understand a chemical formula! Such a search is not restricted to NMR documents. We can however add more conditions to restrict the search, how many conditions we like. For example:
Every time I type a single character the list of results is updated (live). There is also the option of displaying an animated list. It's a cinematic effect that's very characteristic. If you have ever seen iTunes or the iPhone you know what I mean. On my blog I am limiting myself to displaying static pictures, however. Here is how my spectra look like:
And this is only the appetizer! [continues...]
Monday, 17 November 2008
What's New
For more than two years I have been describing application software ("the programs"), and not the operative systems. Sounds obvious? It isn't. I had noticed, in the past, the attempt of a couple of programs (namely the ACD suite and the "NMRnotebook") to substitute the operative system. What they do is to put all your NMR data into a monolithic archive. From that moment on you can't search your files into the normal directory tree: the application program manages everything, substituting for the system. Can they do it better?
I have also seen the opposite phenomenon, that is the appearance of new operative systems that do every kind of things, up to the point to make you feeling that application programs are no more necessary. My preference goes to the latter trend, for a practical reason. When you are in troubles with an operative system, you can find a neighbor or relative that knows it well and that can help you. If you are at work, you can call the IT department. If your troubles arise from the application software, instead, you don't know whom you can turn to. That's why I prefer doing more things than possible with the operative system, if I am allowed.
While I will be describing a specific OS, I am writing for everybody: it's the idea that counts, not the implementation.
Now, in my life I have studied only two OS. The first one was called "IBM-DOS" and the second one "MS-DOS". It happened in an era when the computers included heavy and bulky printed manuals. I have been commuting for half of my life, so I had plenty of opportunities to read paper manuals (over and over again). I am not using those OS any more and I have forgotten what I had learned. I have come in touch with the modern systems, but still feel like a stranger (I haven't found the new manuals yet!). Last week I have begun working with Mac OS 10.5.5. It resembles the old version 7 that I was using in the early 90s, so it looks familiar to me. I have tried to read the installation manual, which shows a few things you can do but doesn't tell how to do them. It only explains how to install the system. I am learning by practice.
The rationale is that customers don't know what to do during the endless installation process, so they are given a manual to spend their time with. Unfortunately, you can read as slowly as you possibly can, but the installation will always be slower than you. To give you an idea, the whole manual, including the unreadable license agreement, weights 94 g.
What has this to do with NMR? Well, this OS seems to be almost ready to handle NMR data out of the box. I want to show you the technologies that I have explored so far, and they are enough to write posts for a week. Mainly I will describe two commands: "Get File Info" and "Find...", that are so ancient I believe they have always been there, with the same keyboard shortcuts (maybe under a different menu). What's new? Now you can install custom plug-ins for those commands. The operative system will instantly become NMR-savvy. Writing a plug-in is not terribly complicated. The Apple site gives you all the tools, libraries, instructions, examples and templates you need. You can write a plug-in in an afternoon. If you have more time, with the same tools you can even write a complete NMR program. No need to look around for the FFT algorithm, it's already a component of the OS. Of course, it has been put there to manipulate sounds, not to process NMR spectra. If you can't write a line of code and want everything ready and free... then you are lucky! What I will be showing during this week can be done with freely available plug-ins. You don't need to know how to write them.
Let me clarify my intent. It's not that I am supporting Apple. I think it's a greedy corporation, no better than Microsoft or IBM. Their products are over-priced in the U.S. and sold at an outrageous price elsewhere. I would rather encourage you to stick to your old hardware and software. (Beware that programs written for System 7 are not compatible with 10.5). Nonetheless, it's nice to be curious about the new technologies. What I have discovered last week sounded new to me, probably is well known to you, surely will become normal practice in the near future. Enough said, for today [continues...].
I have also seen the opposite phenomenon, that is the appearance of new operative systems that do every kind of things, up to the point to make you feeling that application programs are no more necessary. My preference goes to the latter trend, for a practical reason. When you are in troubles with an operative system, you can find a neighbor or relative that knows it well and that can help you. If you are at work, you can call the IT department. If your troubles arise from the application software, instead, you don't know whom you can turn to. That's why I prefer doing more things than possible with the operative system, if I am allowed.
While I will be describing a specific OS, I am writing for everybody: it's the idea that counts, not the implementation.
Now, in my life I have studied only two OS. The first one was called "IBM-DOS" and the second one "MS-DOS". It happened in an era when the computers included heavy and bulky printed manuals. I have been commuting for half of my life, so I had plenty of opportunities to read paper manuals (over and over again). I am not using those OS any more and I have forgotten what I had learned. I have come in touch with the modern systems, but still feel like a stranger (I haven't found the new manuals yet!). Last week I have begun working with Mac OS 10.5.5. It resembles the old version 7 that I was using in the early 90s, so it looks familiar to me. I have tried to read the installation manual, which shows a few things you can do but doesn't tell how to do them. It only explains how to install the system. I am learning by practice.
The rationale is that customers don't know what to do during the endless installation process, so they are given a manual to spend their time with. Unfortunately, you can read as slowly as you possibly can, but the installation will always be slower than you. To give you an idea, the whole manual, including the unreadable license agreement, weights 94 g.
What has this to do with NMR? Well, this OS seems to be almost ready to handle NMR data out of the box. I want to show you the technologies that I have explored so far, and they are enough to write posts for a week. Mainly I will describe two commands: "Get File Info" and "Find...", that are so ancient I believe they have always been there, with the same keyboard shortcuts (maybe under a different menu). What's new? Now you can install custom plug-ins for those commands. The operative system will instantly become NMR-savvy. Writing a plug-in is not terribly complicated. The Apple site gives you all the tools, libraries, instructions, examples and templates you need. You can write a plug-in in an afternoon. If you have more time, with the same tools you can even write a complete NMR program. No need to look around for the FFT algorithm, it's already a component of the OS. Of course, it has been put there to manipulate sounds, not to process NMR spectra. If you can't write a line of code and want everything ready and free... then you are lucky! What I will be showing during this week can be done with freely available plug-ins. You don't need to know how to write them.
Let me clarify my intent. It's not that I am supporting Apple. I think it's a greedy corporation, no better than Microsoft or IBM. Their products are over-priced in the U.S. and sold at an outrageous price elsewhere. I would rather encourage you to stick to your old hardware and software. (Beware that programs written for System 7 are not compatible with 10.5). Nonetheless, it's nice to be curious about the new technologies. What I have discovered last week sounded new to me, probably is well known to you, surely will become normal practice in the near future. Enough said, for today [continues...].
Sunday, 26 October 2008
ProSpect
A rare event: I have found an NMR program that's been a pleasure to inspect. It comes with an HTML manual (with pictures) and sample data. These two ingredients remove the usual obstacle for learning (you rarely guess right how to arrive to a frequency domain spectrum). In this case, instead, I could easily open one of the included sample spectra, because they come with their own processing scripts, and experiment with the buttons (relying on the help of the yellow tips). It's clear that they spent their time and money in making this program. It's well done.
The program is called ProSpect ND and comes from Utrecth. It's completely free. In theory, it's cross-platform. I have tested the Windows version.
Why isn't it more famous? Well, to start with the name, it is focused on multi-dimensional spectroscopy and favors serious processing and flexibility over simplicity of use. You realize this fact from the very beginning. To open a spectrum (Bruker or Varian, no other format is recognized) you must first convert it into the ProSpect format with a script; it's not trivial.
The program also includes all the routines to process and analyze a 1D spectrum. The graphical layout is, well, arguable. For example, the peak-picking labels tend to overlap with each other.
Speaking of 1D, LAOCOON is also included. Forgive my personal reminiscence: the manual doesn't refer to the first version, as everybody else has always been doing, but to the the last version by Cassidei and Sciacovelli, who happen to be the ones who teached me how to use a spectrometer (and some theory too, in the case of Sciacovelli).
My first impression: they have written a program the way they like it. If you need to print your 1D spectra, I bet you'll have diverging opinions. If you like to spend much time in 2D processing to obtain the optimal results, and the other free alternatives don't satisfy you, chances are that ProSpect ND will.
This product confirms the rule: it takes time and money to make NMR software. If you want it free, you must find a sponsor with large shoulders. There's an important difference that puts ProSpect apart from more famous free programs like the original Mestre-C, NMRPipe, SpinWorks, NPK. Prospect is open source. In the case of NPK I may be wrong. Anyway, you can directly download all the source code of ProSpectND without asking any permission, without registering, without logging in. Guess the language? Phyton? Noo! Java? Noo! C++? Noo! OK, here's an hint: the first date on many source files says 1997.
C? Yes, I like it!
The program is called ProSpect ND and comes from Utrecth. It's completely free. In theory, it's cross-platform. I have tested the Windows version.
Why isn't it more famous? Well, to start with the name, it is focused on multi-dimensional spectroscopy and favors serious processing and flexibility over simplicity of use. You realize this fact from the very beginning. To open a spectrum (Bruker or Varian, no other format is recognized) you must first convert it into the ProSpect format with a script; it's not trivial.
The program also includes all the routines to process and analyze a 1D spectrum. The graphical layout is, well, arguable. For example, the peak-picking labels tend to overlap with each other.
Speaking of 1D, LAOCOON is also included. Forgive my personal reminiscence: the manual doesn't refer to the first version, as everybody else has always been doing, but to the the last version by Cassidei and Sciacovelli, who happen to be the ones who teached me how to use a spectrometer (and some theory too, in the case of Sciacovelli).
My first impression: they have written a program the way they like it. If you need to print your 1D spectra, I bet you'll have diverging opinions. If you like to spend much time in 2D processing to obtain the optimal results, and the other free alternatives don't satisfy you, chances are that ProSpect ND will.
This product confirms the rule: it takes time and money to make NMR software. If you want it free, you must find a sponsor with large shoulders. There's an important difference that puts ProSpect apart from more famous free programs like the original Mestre-C, NMRPipe, SpinWorks, NPK. Prospect is open source. In the case of NPK I may be wrong. Anyway, you can directly download all the source code of ProSpectND without asking any permission, without registering, without logging in. Guess the language? Phyton? Noo! Java? Noo! C++? Noo! OK, here's an hint: the first date on many source files says 1997.C? Yes, I like it!
Friday, 24 October 2008
Students
They say that students buy Macs. Is it true? If it is so, and you are a student, be sure to check this promotion out. It's a full-fledged, up-to-date application, offered at a price that's certainly affordable for any student. It's possible to test the product before buying it, of course.
...and you can even leave your comment here below!
...and you can even leave your comment here below!
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