From owner-chemistry #at# ccl.net Tue Jan 15 10:28:00 2008 From: "Agrafiotis, Dimitris K. PRDUS DAGRAFIO!^!prdus.jnj.com" To: CCL Subject: CCL: Asking for "Usage of C sharp in Computational Chemistry" Message-Id: <-36038-080115102308-17305-ewLo7Rm734N7K6f3yEZRcA]*[server.ccl.net> X-Original-From: "Agrafiotis, Dimitris K. [PRDUS]" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 15 Jan 2008 10:22:59 -0500 MIME-Version: 1.0 Sent to CCL by: "Agrafiotis, Dimitris K. [PRDUS]" [DAGRAFIO**prdus.jnj.com] This is a very timely thread for me for a variety of self-serving = reasons. Frankly, I don't think you will get the right advise in this = forum, as it all boils down to personal preferences and familiarity. I = must confess that I am surprised by the foresight of your advisor. C# is = one heck of a programming language, built on one heck of a platform = (.Net) which runs on 90+% of the world's computers. This is something = that the computational chemisty community never really realized and = exploited. If you want to see what can be done in C#, have a look at our = ABCD paper that was recently published in J. Chem. Info. Model. = (http://pubs.acs.org/cgi-bin/abstract.cgi/jcisd8/2007/47/i06/abs/ci700267= w.html), and go to the section on Third Dimension Explorer (3DX). The = application is written entirely in C#, and its performance and = sophistication are astounding. There is a fair amount of C++ code behind = it, but the .Net framework allows it to be seamlessly integrated with = the rest of the application. This project has received a lot of = attention in the press (see, for example, the highlight in the latest = issue of Nature Reviews: = http://www.nature.com/nrd/journal/v6/n12/full/nrd2471.html), so I think = it's worth reading. You may think that this is more of an "IT" type of = application, but you will be astonished by how much hard-core = computational chemistry algorithms you will find in there. So, if I were = to offer my advise, I would say go with C#. You will become familiar = with an envionment that is poised for dominance in the software = industry, and you will have acquired a modern set of skills that will = differentiate you from most of your colleagues who are still left in = Fortran and Perl :-) Which brings me to the self-serving part. If any of you want to be part = of such an effort (ABCD, that is), have experience in .Net, C#, and C++, = and want to live in Belgium, pleae drop me a note (off line). We have = some job openings in our team there, and we are looking for top = programming talent, with a strong background in computational chemistry, = computational biology and informatics, who are not limited by their = training, are able to work in different problem domains, are skilled in = engaging the users and responding to their needs, and are able to work = as part of a larger team. Hint for Mr. Arafat: there are a lot more = skills that you need to acquire to have a successful career in today's = world. Programming is just one of them. Don't underestimate the others. Best regards, ____________________________________________________ Dimitris K. Agrafiotis, Ph.D. Johnson & Johnson Pharmaceutical Research & Development, LLC 665 Stockton Drive, Exton, PA 19341, USA Tel: (610) 458-6045 Fax: (610) 458-8249 E-mail: dagrafio]*[prdus.jnj.com http://www.dimitris-agrafiotis.com -----Original Message----- > From: owner-chemistry]*[ccl.net [mailto:owner-chemistry]*[ccl.net] Sent: Monday, January 14, 2008 10:13 AM To: Agrafiotis, Dimitris K. [PRDUS] Subject: CCL: Asking for "Usage of C sharp in Computational Chemistry" Sent to CCL by: "Chris Moth" [chris.moth(0)Vanderbilt.Edu] C# is a beautiful language for business software development on the Windows platform. The .NET environment shields software development = > from many problems (opportunities) that lower level languages (C especially) can create. For a nice language to "learn how to program", I would say C# is fine - just as PASCAL was good long ago. You can load Microsoft Visual Studio and be writing your first program very quickly. If you are developing a modern, interactive computational chemistry application with a rich user interface, and you want it to run on a variety of platforms, you might look at Java. Java is a conceptual precursor of .NET - and is perhaps more inherently cross-platform. However, many applications in computational chemistry have no user interface to speak of - and are fundamentally dedicated to computation = of results as quickly as possible. Thus compiled FORTRAN and C (vs interprested Java/C#) are going to haev a role in our field for the forseeable future. But yes, they are very old now. Python is certainly interesting - and I would suggest you look at "chimera" as an example of what has been done with it. I was about to write that Python has not caught on with the main-stream software development community - but a quick search at hotjobs.com for "Python" category=3DTech Jobs shows 600 listings. That's quite impressive. > > Sent to CCL by: "Mahmoud Arafat Ibrahim" [M_Arafat82 * Yahoo.Com] > Dear Dr. / Prof. > In the fact, I am a new researcher in Computational Chemistry Subject = and > I am going to specialized in Drug Design. I have started studying C = sharp > as a programming language as my first step in this new field (it was = an > advise from one professor). After an intermediate step in C sharp, I = am > now confusing about its usage in my new field. Indeed, I found that = all > programs have been used in Computational Chemistry are based on = FORTRAN or > C language. So, I am now hesitating about my step and asking for = advice. > > May you direct me to the best step? > -Stop studying Programming languages as whole where they are = usefulness in > Computational Chemistry. > -Study FORTRAN or C language where they are more abundant in = Computational > Chemistry. > or > -Continue studying C sharp where it is the most modern language. > I hope to read from you as soon as possible. > Sincerely; > M. Arafat, > Chemistry Department, > Faculty of Science, > Minia university, > Egypt.> > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt