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ampakine
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[*] posted on 12-7-2011 at 15:53
Programmer/chemist


I'm studying chemistry in college but I seem to have more of a passion for programming and computer related things so I'm gaining just as much programming and computer skills as I am chemistry skills these days. I want to get into a chemistry/pharmacology related field but I'm wondering if my programming skills will come in useful. I'm getting lots of ideas for ways for developing chemistry software and technology and I don't just mean software for making models such as ChemDraw, I mean developing hardware and software for automating chemistry processes. One example off the top of my head: I could develop a machine that will automatically determine the solubility of a compound in a wide range of different compounds at different temperatures. If I'm not mistaken this kinda thing is usually done manually by a chemist. With the right software a machine could do it far more effectively than a human.

Any other programmers/technophiliacs here?
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[*] posted on 12-7-2011 at 16:25


In my daily work (as a biochemist) I get lots of ideas for automation too. However, in my opinion, the critical factor is: how big is the market for your machine. Either the machine needs to cost a fortune for it to pay your bills, or you have to sell a lot of them. AFAIK, there are not that many occasions when you need to establish the solubility accurately.

Some of the tasks I think are worth automating (ie. I would buy a 10,000+ Euro machine to automate the job):
1. Calibrating pipettes
2. Western blotting
3. transfering samples from vials to 96 well plates




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[*] posted on 13-7-2011 at 09:16


If you like programming and like biology you should aim for bioinformatics.

Pay is good as I understood it, e.g. on projects one might get between $90-300K a year in Norway. You would earn more if you work freelance.

Developing hardware is expensive (my first biotech patent filed two weeks ago), plus there is the thing about patenting your invention, and reading prior art and such as not to be sued.

But yeah, you should get into it.


PS. One tip, next generation sequencing is the big thing and will continue to be so for atleast a decade IMO.




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[*] posted on 13-7-2011 at 09:22


That kind of money....probably not as a postdoc, right? Industry?



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[*] posted on 13-7-2011 at 14:51


Well, a postdoc position in a government place e.g. like the university I work wouldn't get you more than lowest pay they are allowed to give you (those cheap bastards..) which would be less than $90K. We lack a fulltime bioinformatician in our group and so, some use their presious off work time to learn the skill. The reason we lack one is that nobody would take a doctorate and be paid that low, and the reason the administratives gave for the low pay is that none could earn more than their schooling as not to "upset" the balance even if their skill was unique. So yes, one would have to go into the private sector to get to the real money..



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[*] posted on 14-7-2011 at 11:56


Quote: Originally posted by phlogiston  
In my daily work (as a biochemist) I get lots of ideas for automation too. However, in my opinion, the critical factor is: how big is the market for your machine. Either the machine needs to cost a fortune for it to pay your bills, or you have to sell a lot of them. AFAIK, there are not that many occasions when you need to establish the solubility accurately.

Some of the tasks I think are worth automating (ie. I would buy a 10,000+ Euro machine to automate the job):
1. Calibrating pipettes
2. Western blotting
3. transfering samples from vials to 96 well plates


To my mind humands need to forget about volume measuring at all!
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[*] posted on 2-1-2012 at 13:05


Ampakine,

If you attend a university, you should consider taking a graduate course in Computational Chemistry (i don't think they teach it undergrad). This will give you a feel as to what to expect in the emerging computational/programming aspects of chemistry. It's funny you mention developing "machines" or instruments that determine the solubility of compounds in a wide variety of solvents, as this is getting more into the engineering aspect. There are actually clients available that can compute this information for you. You just have to learn how to use them (and often times you're using several to dozens of different programs in conjunction to the client you use to build your molecules). I found the coding to be very frustrating when I was taking this class, because of the amount of errors you generate in trying to pump out calculations (which can take days to run even in a university high-performance computing center). But it's also very fascinating to see what's possible with this software, and what people have done with it. And I see you mentioned pharmacology - this is actually very relevent to modern-drug development/pharmacology as well.
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[*] posted on 2-1-2012 at 17:13


If you want to explore developing hardware, i highly reccomend buying an arduino kit Arduino Website. Ive got one and I have set it up with multiple sensors so I can measure temp, pH, and I can even measure O2 percentage in the air, etc.



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[*] posted on 24-11-2012 at 22:49


The answer:


automation is already a huge part of big-pharma.


I don't just mean autosamplers/injectors or the robotic SP synthesis of DNA/RNA or peptides....


Combinatorial chemistry.... its huge...... its broken down into software and hardware.


the software is bioinformatics + computationa/theoretical chemistry/biochemistry + computer science (+pure math)


typically a big push is to find ways to simulate ab-initio/semi-empirical or semi-classical (for MD) models using whatever algorithm/technique can achieve it....

the goal is to minimize CPU time without unaccetable error.


Hardware is genuinely a fast, automated, testing procedure..... thousands of chemicals can be synthesized using microfluidics (nanomolar quantities) and robotics and automatically shot into HPLC/MS or even NMR in a fully automated process.


typically this does not mean multi-step synthesis of an entire drug molecule.... it means testing 1 step of a proposed synthesis...


when it is used to test the actual drug molecule itself, they will often synthesize thousands of different chemicals with slightly different structures (eg: 2 carbon vs 3 carbon chain.... 5 carbon vs 6 carbon ring... etc), then pass those potential compounds through to a genuine biological/biochemical target (such as a lab-on-chip system) which will give a measurable response depending on the binding efficiency.



the reality is that the field is full of proprietary technology and trade secrets..... some of it is COTS (commercial off the shelf) but most is not.
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[*] posted on 15-2-2014 at 18:48


Not to resurrect an old thread, but it is near the top, so I will respond. I do some computational aspects within drug discovery (including QSAR, data mining and drug docking, primarily), and know a couple others in pharmacology who do much heavier programming than I. While my experience in purely chemical modeling is shallow, I have found much more interaction between in silico and wet pharmacology since transitioning from just chemical synthesis. Neuroscience modeling and some proteomic aspects of pharmacology seem to largely rely on custom single purpose programs despite several great open source suites (ex. NEURON, ADT). I have also found scripts useful in genome annotating, though you can use many publicly accessible resources for that type of work as well, like BLAST, CLUSTAL, etc.
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[*] posted on 10-3-2014 at 02:29


zoombafu: Have you any resources on pH probes and interfacing software for the Arduino? Is there sensors one can use for density of a solution?

I recently was thinking to fit similar sensors to one of my homebrewing containers, see if I could graph pH changes, temp changes in solution over time (along with, if possible, density changes and the likes) but did not know where to start, having never done any work with the Arduino itself before (my programming background being networked applications and kernel modules for Linux). Any advice would be greatly appreciated!

As for OP, the computational chemistry/bioinformatics side of things is supposed to be where a lot of the "serious money" is these days.
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[*] posted on 10-3-2014 at 02:29


zoombafu: Have you any resources on pH probes and interfacing software for the Arduino? Is there sensors one can use for density of a solution?

I recently was thinking to fit similar sensors to one of my homebrewing containers, see if I could graph pH changes, temp changes in solution over time (along with, if possible, density changes and the likes) but did not know where to start, having never done any work with the Arduino itself before (my programming background being networked applications and kernel modules for Linux). Any advice would be greatly appreciated!

As for OP, the computational chemistry/bioinformatics side of things is supposed to be where a lot of the "serious money" is these days.
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[*] posted on 23-3-2014 at 15:49
Nice one


Perhaps I'm wrong, but in my opinion programming and chemistry have nothing to do with each other. If you are interested in both sciences, perhaps that means that you have a drive passion for learning difficult things.
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[*] posted on 26-3-2014 at 09:34


How about in-organic chemistry? Are there any suggestions as to what kinds of programs would be useful for even amateur chemists?



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[*] posted on 28-4-2014 at 11:59


I do some programming myself too, I see massive potential in the area of computational chemistry, especially since its only gonna become more and more commonly used as computers become more powerful. As someone above mentioned, its mighty useful for QSARs, most chemists aren't programmers so they don't know how to write a script that will automatically generate a thousand Gaussian input files containing slightly modified z-matrices and compiling it all into a batch file that Gaussian will run automatically. Then on top of that, you can do data mining on it, and find correlations that would be difficult for a human to spot.

The Volatile Chemist: Yeah, I bet there are plenty of applications. You can predict reaction pathways with Gaussian, so that'd be one use for an amateur chemist. I haven't got into computational chem much yet, I don't know how to predict things like solubilities, not sure if the technology is even there yet but that would be very useful for amateur chemists (any chemists for that matter). Someone above mentioned an arduino kit, I clicked the link and that looks awesome. I don't know anything about electronics, I wanna get into it because I would be able to write programs to control the machines. You could build something like an automatic columning machine, once it detects that a product is coming out of the column, it waits for it to elute fully, then switches container. I'm getting a bit carried away here though, I have no idea how I could do that.

Quote: Originally posted by flashmanc  
Perhaps I'm wrong, but in my opinion programming and chemistry have nothing to do with each other. If you are interested in both sciences, perhaps that means that you have a drive passion for learning difficult things.

If you take up programming, you'll see it differently. The physical world is kind of like a program, everything has an algorithm to it. Thats what QSARs is all about, finding those algorithms/correlations. Chemistry and programming are two separate fields for now, but in the future they'll be a lot more interlinked. Computational chemistry will make a lot of practical experiments obsolete, which is a good thing because it'll mean less wasting of resources, and in medicinal chemistry, it'll mean less need for animal testing. The main issue now is that it takes such a long time to run calculations on big molecules, but that will change. Look at how far computing technology has advanced in the past 10 years.

[Edited on 28-4-2014 by CrimpJiggler]
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[*] posted on 29-4-2014 at 22:54


Quote: Originally posted by flashmanc  
Perhaps I'm wrong, but in my opinion programming and chemistry have nothing to do with each other. If you are interested in both sciences, perhaps that means that you have a drive passion for learning difficult things.

This simply is not true. Programming (and more general: data aquisition and control) becomes more and more important in chemistry. I hardly can imagine a single chemical plant which is not leaning heavily on ICT, also for its core processes. Control and monitoring software makes plants more reliable, makes it easier to precisely control amounts of reagents to be mixed and allows an operator to peek into the process at great depth.

And what to think of all modern measurement and analysis equipment, used by chemists. These things really are full of software, for converting raw measurement data to intelligible data, presenting results on screens, controlling the measurement itself.

Software also becomes more and more important in research, as mentioned by the previous poster. Analysis of large molecules can be done by means of advanced molecular models which are simulated by software. This requires tremendous amounts of processing power, but computers still are becoming faster rapidly and at the moment there also is a development towards more and more parallellism (multiple cores) and at the software level the use of multiple cores is exploited more and more.




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[*] posted on 30-4-2014 at 01:48
programming and chemistry


I lost my baby teeth coding MAC drivers for industrial imaging scanners. I have written knowledge management systems, computer vision systems, built military weapons controllers, and everything else computer related under the sun, for over 30 years. IMHO programming is vastly interesting and very much related to the scientific method. Your thoughts must be absolutely precise to program well. Programming feels mathematical in the states of concentration it requires. Programming machine to machine, the internet of things, the recent influx of interesting tiny computers, cell phones, raspberry pi's, aurdrino's, etc, is changing the world. I guarantee a foundation in software development will make you more effective at any technical or scientific career that you choose. I guarantee that writing quality code makes you a better scientist, and therefore, a better chemist.
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[*] posted on 15-5-2014 at 10:15


Chemistry and computing certainly have strong and interesting interconnections (my entire job/career is based on this) :) Quickly surveying this connection-- a vast array of computational methods in chemistry and biochemistry have been developed for creating 'realistic' models of molecules, to be able to predict reactivity or properties. Experimental chemistry results provide feedback to develop these models, and in turn, once the models are refined sufficiently, they're able to make high-accuracy predictions of new molecules or reactions (as long as the inherent chemistry of the 'new' system is still appropriate for the set of approximations being used in the model). Also, when interesting phenomena in chemistry or biochemisty are observed, it is often hard to unravel a molecular-level explanation in the lab, but through these precisely-controlled computational models, we can get a picture of what may be happening and improve our knowledge of the basic sciences.

Computational chemistry ends up being a very powerful tool for its predictive or explanatory power, and also can save a lot of money in academic or industrial research settings, by just burning some CPU hours, to reduce the number of molecules or reactions an experimentalist may need or want to test in the lab (reducing both raw material costs, and of course human *time*)

Opportunities for careers in this area are intriguingly diverse, from predicting new catalysts, new material properties, understanding basic organic chemistry reactivity, improving photovoltaics, understanding enzyme mechanisms, ...( I'll refrain from continuing an overzealous list-- it's truly an endless list of fascinating applications, to fill far too many lifetimes :) )
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[*] posted on 15-5-2014 at 12:33


Quote: Originally posted by Dagny  
Chemistry and computing certainly have strong and interesting interconnections (my entire job/career is based on this) :) Quickly surveying this connection-- a vast array of computational methods in chemistry and biochemistry have been developed for creating 'realistic' models of molecules, to be able to predict reactivity or properties. Experimental chemistry results provide feedback to develop these models, and in turn, once the models are refined sufficiently, they're able to make high-accuracy predictions of new molecules or reactions (as long as the inherent chemistry of the 'new' system is still appropriate for the set of approximations being used in the model). Also, when interesting phenomena in chemistry or biochemisty are observed, it is often hard to unravel a molecular-level explanation in the lab, but through these precisely-controlled computational models, we can get a picture of what may be happening and improve our knowledge of the basic sciences.

Computational chemistry ends up being a very powerful tool for its predictive or explanatory power, and also can save a lot of money in academic or industrial research settings, by just burning some CPU hours, to reduce the number of molecules or reactions an experimentalist may need or want to test in the lab (reducing both raw material costs, and of course human *time*)

Opportunities for careers in this area are intriguingly diverse, from predicting new catalysts, new material properties, understanding basic organic chemistry reactivity, improving photovoltaics, understanding enzyme mechanisms, ...( I'll refrain from continuing an overzealous list-- it's truly an endless list of fascinating applications, to fill far too many lifetimes :) )


The Main problem for me is that I'm a programmer (Per-say, I haven't taken real classes, just read), and an uneducated amateur Chemist. I don't know how to data mine chemistry subjects, I know nothing of molecular theories, etc. I need someone to tell me what can be done and how to do it, or at least give me a book on it :) I'd love to write programs for chemistry, but where can I find books on predicting catalyst properties in chemicals? I don't care how complex the subjects are, but I am yet to find an explanation.




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rskennymore
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[*] posted on 25-5-2014 at 04:08


Quote: Originally posted by The Volatile Chemist  

The Main problem for me is that I'm a programmer (Per-say, I haven't taken real classes, just read), and an uneducated amateur Chemist. I don't know how to data mine chemistry subjects, I know nothing of molecular theories, etc. I need someone to tell me what can be done and how to do it, or at least give me a book on it :) I'd love to write programs for chemistry, but where can I find books on predicting catalyst properties in chemicals? I don't care how complex the subjects are, but I am yet to find an explanation.


I'm more or less in the same boat here. I'm a software engineer by trade, I've been developing java for the better part of 5 years now. I've been interested in chemistry for most of my life but have never taken the plunge into trying to understand it at a fundamental level until recently. I've sorta just started writing a molecular geometry engine and am fleshing it out as I learn more about how atoms interact. Mostly reading wiki articles and the vast sea of pages you can find from google searching. I think trying to understand how to predict catalyst properties without understanding atomic models would be putting the carriage before the horse, that might just be me though.
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[*] posted on 25-5-2014 at 06:13


Quantum chemistry calculations are no joke. This is where not only must one be a good programmer writing in a low-level environment for speed, one must be a good mathematician, and physicist/physical chemist. The things people do to turn abhorrent calculations into bit shifts and things are absolutely mind-bending(to me but I'm a laymen). Even the 'fast inverse' square root that was used in the quake 3 engine took my breathe away the first time I saw it hahaha(http://betterexplained.com/articles/understanding-quakes-fas...). I have written a few applications with my background in 3-D programming related to the quantum nature of single atomic orbitals. It wasn't difficult but it did take time to get everything right(3-4 days), and on that level well, it wasn't useful more demonstrative.

There are tons of resources for this kind of information.
Start with things like - http://vergil.chemistry.gatech.edu/courses/chem6485/pdf/Elec...

Move to things about numerical methods for PDE's. Brush up heavily on linear algebra, series, etc... Remember the N-body problem is not your friend (if you solve it give me a call :P). So there are things like the Hartree-Fock,

http://en.wikipedia.org/wiki/Hartree%E2%80%93Fock_method
http://en.wikipedia.org/wiki/Post-Hartree%E2%80%93Fock
http://en.wikipedia.org/wiki/Unrestricted_Hartree%E2%80%93Fo...

But oh which theory to use, here's one that people have been using lately to my understanding,
http://en.wikipedia.org/wiki/Density_functional_theory
Of course there are literally hundreds if not thousands of techniques to implement DFT in different ways into soft-ware...

You'll also need your thermodynamics down. I don't mean ΔG = ΔH - T*ΔS. Useful predictions can be performed on an electronic basis, but turning that into thermodynamics is very important... Edit - Oops just saw you were interested in catalysts. Definitely going to want to be firm on kinetics! Turning the PDE's into ODE's etc. Steady state approximations. Hmmm, could see an algorithm for that, would be an effort though. I'm sure people have already developed clever ways around a lot of this.

Might be easier to start with some open-source ab initio chemistry library or something similar. Then again if you don't know what the algorithms are doing, it could be a whole lot harder to implement them.

If you wish to implement visualization in 3 space, you'll have to decide on DirectX or OpenGl. I prefer OpenGl as it's cross plat-form. GLSL is also just slightly more intuitive to me personally than HLSL. I'm sure many people would scoff at that, and say Direct X. From there, either write you're own graphics engine or again find an open source one, hopefully tailored for speed and modify what you need.

For the processing of calculations I think a lot of people are actually doing this on GPU's now days rather then the CPU. http://en.wikipedia.org/wiki/Molecular_modeling_on_GPUs

Hope this gives you some ideas.

[Edited on 25-5-2014 by smaerd]

[Edited on 26-5-2014 by smaerd]




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The Volatile Chemist
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[*] posted on 26-5-2014 at 07:05


That indeed was what I needed! It'll get me started this summer (School's almost out for me, then I'll have much more free time!).
As I side note, I'm working on a scientific 'calculator'/'assistant' console program. It's tailored to my needs, but when I'm finished it may find use for others.




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[*] posted on 27-5-2014 at 06:41
amazing super chemistry software


At the recommendation of a friend I have been learning about,
http://www.chemaxon.com/
MarvinSketch.
I have learned more o-chem using this program first, then looking up what I don't understand in my books and online. If one is interested in chemistry software, this program is quite interesting.
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[*] posted on 27-5-2014 at 17:17


Marvin sketch is great for laying out reaction schemes, quick modeling, theoretical calculations, etc. It does have a nice resonance structure creator which I have used for quickly checking substrates for dominant resonance forms for possible reactivity. Not really sure how it could teach organic chemistry though. It is my preferred soft-ware suite though, so I feel you there.



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[*] posted on 17-7-2014 at 09:09


Quote: Originally posted by ampakine  
I'm studying chemistry in college but I seem to have more of a passion for programming and computer related things so I'm gaining just as much programming and computer skills as I am chemistry skills these days. I want to get into a chemistry/pharmacology related field but I'm wondering if my programming skills will come in useful. I'm getting lots of ideas for ways for developing chemistry software and technology and I don't just mean software for making models such as ChemDraw, I mean developing hardware and software for automating chemistry processes. One example off the top of my head: I could develop a machine that will automatically determine the solubility of a compound in a wide range of different compounds at different temperatures. If I'm not mistaken this kinda thing is usually done manually by a chemist. With the right software a machine could do it far more effectively than a human.

Any other programmers/technophiliacs here?


Can you write a mod/program and create system for doing routine quality control analysis in the chemical labs for industry?
If you do , it would be much more helpful for industrialists...




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