Question: How To Learn To Build A Bioinformatics Oriented Web Site
1
gravatar for Paris
6.4 years ago by
Paris10
Paris10 wrote:

Hi, am absolutely new to programming and bioinformatics. Am building a web/server for a research project and would need every assistance i can get here. I will try to list my challenges as much as i can.

These are the languages i have learnt and am planning to use them. I dont have much time to learn new languages.

Web server/application server        : visual studio
Scripting Language                       : c# 
Front-End                                     : XHTML/CSS 
RDBMS                                        :SQL.
  1. I cant find a standard way to classify proteins, and since i need to present a good database design i dont know where to start from.
  2. I want to develop a web application that can give a 3Dstructure of proteins, using c#.

Any help would make a great help.

Thanks in advance.

Ken

ADD COMMENTlink modified 6.4 years ago by vijay1.5k • written 6.4 years ago by Paris10
7
gravatar for Istvan Albert
6.4 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

Your way of thinking guarantees that you will be unsuccessful. You can't go into any project with the mindset of not wanting to learn something new.

At the same time just about everything that you list is incorrect: Visual Studio is not an application server. C# is not a scripting language, XHTML is not a front end. SQL is not a RDBMS.

ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by Istvan Albert ♦♦ 81k
4

You can't go into any project with the mindset of not wanting to learn something new.

This should be made into a bumper sticker for everyone, not just for bioinformaticians.

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by Josh Herr5.6k
7

Where does op state he doesn't want to learn something new? " I dont have much time to learn new languages." That's reasonable if you have just started. The mindset of the op is not the problem. The problems are in fact that: 1. the task is several sizes to large for a beginner, beginners should start with easier practice tasks. 2. the task is already solved by PDB and 3. op got pushed in a situation (sounds to me at least), where he is supposed to do something which is way above his head and is weakly defined. As an absolute beginner, it is natural to be unable to judge the requirements of such an undertaking correctly, let alone figuring out a way to solve them. Therefore, this is a sign of poor management and supervision, nothing else. This would certainly include total absence of a supervisor, maybe out of a spontaneous idea.

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by Michael Dondrup46k
1

While it is true that the OP does not explicitly state that she/he does not want to learn new concepts, they are actually implying it indirectly. The overall sentiment that I want to get across is that the less someone knows about a domain the more open they need to be embrace new knowledge/information. Looking for solutions within the strict confines of existing skills/abilities will almost certainly be unsuccessful.

ADD REPLYlink written 6.4 years ago by Istvan Albert ♦♦ 81k
4
gravatar for Neilfws
6.4 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

I think the answer to the "how to learn" part of your question is "take some classes in bioinformatics and/or programming". It's clear that you lack the basic skills required to formulate and answer a research problem. This is not something that you can simply "pick up" with no training.

ADD COMMENTlink written 6.4 years ago by Neilfws48k
4
gravatar for vijay
6.4 years ago by
vijay1.5k
Chennai
vijay1.5k wrote:

I would like to appreciate you for your initiative to come up with a bioinformatics application. Even before you start building your web server, I would strongly suggest you to jot down your objectives and match them to your technical skills. Then try to fill in the gaps. Also try to address the crux of the requirement rather than beating around the bush. To start with , go through the works that have been done already on addressing the objectives that you have put up. Then you can arrive at a decision of how you can project your version of those. For instance, when you say " I want to develop a web application that can give a 3Dstructure of proteins, using c# " Does that mean your server will generate structures of proteins if their sequences are submitted or will it just be a database of protein structures ?? Why would do create something that already exists with exception to the coding language..

So define your goals descriptively well in advance, Then try to check how the technologies that you know could be used to achieve them. You have many tutorials that can teach you the basics .

Best of Luck!!!

ADD COMMENTlink written 6.4 years ago by vijay1.5k
2
gravatar for Michael Dondrup
6.4 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

I want to develop a web application that can give a 3Dstructure of proteins...

So maybe you want to use PDB, problem solved?

ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by Michael Dondrup46k
2
gravatar for SES
6.4 years ago by
SES8.2k
Vancouver, BC
SES8.2k wrote:

One approach would be to use Visual Studio to build your .NET application and use something like Jmol for displaying the protein structures. There is a JavaScript library for Jmol that may be helpful for incorporating this tool into your workflow. For the database design, I would start by looking at the PDB file format and do some research about how the different protein data banks store this information. For parsing the files, you can probably find a library written in C and then you could incorporate this into your application with C#.

If this is some kind of short-term project goal (or assignment), you may want to focus on just building the application. I don't want to be discouraging, but it's not realistic to think you can build a web-based tool that is biologically useful in a short amount of time, especially with no relevant experience. On the other hand, you'll probably gain a much greater understanding and appreciation for the existing tools when you see how much work went into them.

ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by SES8.2k
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