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URL: C# in developing bioinformatics programming object model
Submitted by Deying Kong; posted on Thursday, October 03, 2002 (17 comments)
Currently most of software tools and programming models were developed with Perl or Java under the Unix system. Millions of Windows programmers are blocked from accessing these programming objects. Do they need to learn Unix and Perl? Many biologist are familiar with the easy-to-use Windows system. Can they spend less time learning Windows solutions? I am exploring the power of the Windows platform and the modern, elegant language C# (a cross platform .Net solution development language) and using them to develop a proper hierarchical object model and analysis tools.
You can visit this web site to check on the advancing project:
http://globetrack.dnsalias.com/bioinformatics/
You are very welcome to post your ideas and comments on this web site.
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Expanded view | Monitor forum | Save place
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why would you not want to learn unix? its called bioINFORMATICS for a reason. learn unix, enjoy yourself, become a better human being.
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Why not support Unix/Linux? Java, Perl or Python are also elegant and powerfull and freely avaible. Linux can be as easy as windows, with a very good GUI too, its just a matter of time to Linux become the choice in most molecular biology labs. And, Linux is much more stable and reliable than windows, if you are doing a research, you d ont want a blue screen error message when are saving a special sequence or analysis results or reset your computer after each run of a local BLAST search to free memory.
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If there is people coding bioperl, there is people coding biopython. That is real redundance.
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Bioperl and Biopython have different approaches. Read the documentation :-)
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C# is cross platform? I thought C# was .NET
specific, which means it will run in any OS
that Microsoft sells.
Its only a beta-test compiler, but the compiled
C# code I've seen takes up a large memory footprint when compared to the gnu gcc or g++.
So far, C# has all the bloat and overhead of Java
and none of the platform independence.
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Yes, Microsoft developed C#, BUT it's an ECMA standard, so you are free to port it to Linux, for example. And that's exactly what Miguel de Icaza did with the Mono Project (www.go-mono.com). The conclusion: C# is cross plattform! And the .NET Framework is a great application plattform with rich functionality. So my opinion is, it's good for Linux to have such an API!
Concerning this project, I'll find it very interesting and a good idea. This will bring Bioinformatic to thousands of (Windows-)Developer or vice versa.
So, good luck!
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Yes, Microsoft developed C#, BUT it's an ECMA standard, so you are free to port it to Linux, for example. And that's exactly what Miguel de Icaza did with the Mono Project (www.go-mono.com). The conclusion: C# is cross plattform! And the .NET Framework is a great application plattform with rich functionality. So my opinion is, it's good for Linux to have such an API!
Concerning this project, I'll find it very interesting and a good idea. This will bring Bioinformatic to thousands of (Windows-)Developer or vice versa.
So, good luck!
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I think we should support GNU/Linux, and perl, not only because it`s currently very easy to use and with a nice graphic environment (please see www.gnome.org), but because it is FREE, I mean, it follows the philosophy that thinks that knowledge should be humanity's patrimony, and not
controled by a small group.
We can't say the same about Windows/C#/.NET.
Supporting free software is not only getting the best (although it is too). It is supporting freedom
(sorry for my awful english...)
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Dear deying,
I can see that you are probably an expert in bioinformatics. But, it is apparent you are not one in software technology.
There is nothing wrong in you considering a C# based bioinformatics tool/toolset. But, the reasons you provide are wrong and plain misleading. That, my friend is very irresponsible.
Any software in Perl and Java can be easily executed on windows platfrom. Runtime environments - JVM for Java and Perl interpreter for Perl are easily available for windows. Also, if enduser usability was the a concern, one expects that you have a look at Mac systems too.
Nevertheless, just say you are looking a C# and .Net just because you would like to explore the possibility. I request you to refrain from making statements which hurt your credibility.
Take care.
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Boy did he sum it up. You should have checked to see if Java and Perl run on Windows before making those embarassing for you statements.
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You are missing the point about Perl, *nix and Windows. What should be important to the bioinformatics community is that the source-code of the programs we use be open. As a scientist, I will not use reagents whose components I cannot have access to; I want to know the composition of the protease inhibitor cocktail I use making nuclear extracts and what regents are in the coctail I use to label cRNA (kits are a fact of life, but I won't use a kit that isn't based on a protocol that is published somewhere that I can see it, preferrably in a peer reviewed journal).
The same holds true for the software I use to analyze data; having access to the algorithms used to classify the results of an array experiment or to design a set of unique oligos to print on an array is a requirment before I will use the programs.
Microsoft has not been a supporter of open source software, and has, according to memos released from inside Microsoft, actively tried to stop this movement. Becuase of this attitude, Microsoft likes to use propietary processes that make porting to a different os difficult.
That said, there are open source C compilers and java runtime environments available for windows, and programs written in java run on windows, if you install the latest Sun Java and not the old version supplied by Microsoft (another example of Microsofts efforts to squelch open source, see the news articles about the Sun suit against Microsoft that is taking place right now).
And there are perl, python, and tcl interpretors/compilers for Windows (see activestate website). More importantly, there are a many software developers who are working on the bioperl, biopython, and biojava projects whose goal is to facilitate the development of portable code, rather than having to reinvent code for everyday tasks over and over again.
You say that most software is written for Unix OS in perl and Java. I think that if you look, you will find that much of the commercial, proprietary bioinformatics software is written for windows. This is a good business plan because companies know that Microsoft has the lions share of the desktop market. It only makes sense to write software for the most common desktop OS so you can sell a license for every desktop that needs to use the program. That's a good business plan, but not necessarily good for developing bioinformatics projects.
While I wouldn't think of discouraging your investigations into C# and .Net, I think you ought to take a close look at the opensource projects (like bioperl, biopython, biojava, bioConductor, R, genex and many many more), and see what people are actually doing in bioinformatics rather than to assume that because it isn't based around a microsoft format it is either too hard or done badly.
btw, this little form will only allow me to choose the value "Anonymous" for "Post as". I'm sure that this is just a problem with browser compatibility, but its another example of why we need to have some common ways to do things, whether we use linux, MS, solaris, or a macintosh.
srlasky
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could we run c# on unix Os? I knew it is designed to work on .net platform.
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could we run c# on unix Os? I knew it is designed to work on .net platform.
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Check out the mono project
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I am interested in the following site:
http://globetrack.dnsalias.com/bioinformatic
s/
but I can't get in: unauthorized access
bye,
Kevin O'Neill
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